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(-) Description

Title :  STRUCTURE OF GLYCOSYLATED GLUTAMINYL CYCLASE FROM DROSOPHILA MELANOGASTER
 
Authors :  P. Kolenko, B. Koch, D. Ruiz-Carilo, M. T. Stubbs
Date :  21 May 12  (Deposition) - 29 Aug 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha/Beta Hydrolase, Pglu Formation, Pe, Alzheimer'S Disease, Pyroglutamate, Pglu-Amyloid, Glycosylation, Transferase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Koch, P. Kolenko, M. Buchholz, D. Ruiz Carrillo, C. Parthier, M. Wermann, J. U. Rahfeld, G. Reuter, S. Schilling, M. T. Stubbs, H. U. Demuth
Crystal Structures Of Glutaminyl Cyclases (Qcs) From Drosophila Melanogaster Reveal Active Site Conservation Between Insect And Mammalian Qcs.
Biochemistry V. 51 7383 2012
PubMed-ID: 22897232  |  Reference-DOI: 10.1021/BI300687G

(-) Compounds

Molecule 1 - CG32412
    Chains: A, B
    EC Number: 2.3.2.5, 3.4.-.-
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Common: PICHIA PASTORIS
    Expression System Plasmid: PPICZALPHAB
    Expression System Strain: X33
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 29-340
    Gene: QC, CG10487, CG32412, DMEL_CG32412
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: GLUTAMINYL-PEPTIDE CYCLOTRANSFERASE, GH11174P

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Asymmetric Unit (6, 14)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GOL1Ligand/IonGLYCEROL
3MAN4Ligand/IonALPHA-D-MANNOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PBD2Ligand/Ion1-(3,4-DIMETHOXYPHENYL)-3-[3-(1H-IMIDAZOL-1-YL)PROPYL]THIOUREA
6ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1BMA-1Ligand/IonBETA-D-MANNOSE
2GOL1Ligand/IonGLYCEROL
3MAN-1Ligand/IonALPHA-D-MANNOSE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PBD1Ligand/Ion1-(3,4-DIMETHOXYPHENYL)-3-[3-(1H-IMIDAZOL-1-YL)PROPYL]THIOUREA
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GOL-1Ligand/IonGLYCEROL
3MAN4Ligand/IonALPHA-D-MANNOSE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PBD1Ligand/Ion1-(3,4-DIMETHOXYPHENYL)-3-[3-(1H-IMIDAZOL-1-YL)PROPYL]THIOUREA
6ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:131 , GLU A:171 , HIS A:297 , PBD A:402BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWAREASP A:131 , GLU A:170 , GLU A:171 , TRP A:176 , ASP A:218 , ASP A:271 , PHE A:292 , TRP A:296 , HIS A:297 , ZN A:401 , HOH A:1268BINDING SITE FOR RESIDUE PBD A 402
03AC3SOFTWAREGLU A:38 , ASN A:42 , TRP A:308 , NAG A:404 , HOH A:1058 , HOH A:1231BINDING SITE FOR RESIDUE NAG A 403
04AC4SOFTWARENAG A:403 , HOH A:1216BINDING SITE FOR RESIDUE NAG A 404
05AC5SOFTWARETYR A:231 , ASN A:233 , LEU A:278 , PRO A:283 , VAL A:284 , HOH A:1158 , HOH A:1165 , HOH A:1198BINDING SITE FOR RESIDUE GOL A 405
06AC6SOFTWAREASP B:131 , GLU B:171 , HIS B:297 , PBD B:402BINDING SITE FOR RESIDUE ZN B 401
07AC7SOFTWAREARG A:85 , ASP B:131 , GLU B:170 , GLU B:171 , TRP B:176 , ASP B:218 , ASP B:271 , PHE B:292 , TRP B:296 , HIS B:297 , ZN B:401 , HOH B:537 , HOH B:760BINDING SITE FOR RESIDUE PBD B 402
08AC8SOFTWAREGLU B:38 , ASN B:42 , TRP B:308 , NAG B:404 , HOH B:795BINDING SITE FOR RESIDUE NAG B 403
09AC9SOFTWARENAG B:403 , BMA B:405 , HOH B:516 , HOH B:696 , HOH B:794BINDING SITE FOR RESIDUE NAG B 404
10BC1SOFTWAREGLN A:68 , NAG B:404 , MAN B:406BINDING SITE FOR RESIDUE BMA B 405
11BC2SOFTWAREBMA B:405 , MAN B:407 , MAN B:409 , HOH B:630 , HOH B:758 , HOH B:794BINDING SITE FOR RESIDUE MAN B 406
12BC3SOFTWAREMAN B:406 , MAN B:408 , HOH B:796BINDING SITE FOR RESIDUE MAN B 407
13BC4SOFTWAREGLY A:74 , GLN A:151 , ARG A:155 , MAN B:407BINDING SITE FOR RESIDUE MAN B 408
14BC5SOFTWAREALA B:304 , ASN B:305 , LEU B:306 , HIS B:307 , MAN B:406 , HOH B:516 , HOH B:665BINDING SITE FOR RESIDUE MAN B 409

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:113 -A:136
2B:113 -B:136

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:131 -Ser A:132
2Thr A:290 -Pro A:291
3Asp B:131 -Ser B:132
4Thr B:290 -Pro B:291

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F9U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F9U)

(-) Exons   (0, 0)

(no "Exon" information available for 4F9U)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeeeeeeeee...eeeeeeeeeeee.....eeeeeeee.................hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..............hhhhhhhhhhhhhh...hhhh.eeeeeeee........eee.hhhhhhhhhhhhhhhhhhhhh.........eeeee........hhhhhh....eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f9u A  33 QWRDDEVHFNRTLDSILVPRVVGSRGHQQVREYLVQSLNGLGFQTEVDEFKQRVPVFGELTFANVVGTINPQAQNFLALACHYDSKYFPNDPGFVGATDSAVPCAILLNTAKTLGAYLQKEFRNRSDVGLMLIFFDGEEAFKEWTDADSVYGSKHLAAKLASKRSPRNIDRIEVLVLLDLIGARNPKFSSFYENTDGLHSSLVQIEKSLRTAGQLEGNNNMFLSRVSGGLVDDDHRPFLDENVPVLHLVATPFPDVWHTPRDNAANLHWPSIRNFNRVFRNFVYQYLKRHTSPVNLRF 337
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192    || 209       219       229       239       249       259       269       279       289       299       309       319       329        
                                                                                                                                                                                              197|                                                                                                                                    
                                                                                                                                                                                               205                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeeeeeeeee...eeeeeeeeeeee.....eeeeeeee.................hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..............hhhhhhhhhhhhh......hhhh.eeeeeeee............hhhhhhhhhhhhhhhhhhhhh......................hhhhhh....eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f9u B  32 SQWRDDEVHFNRTLDSILVPRVVGSRGHQQVREYLVQSLNGLGFQTEVDEFKQRVPVFGELTFANVVGTINPQAQNFLALACHYDSKYFPNDPGFVGATDSAVPCAILLNTAKTLGAYLQKEFRNRSDVGLMLIFFDGEEAFKEWTDADSVYGSKHLAAKLASKRSLAPRNIDRIEVLVLLDLIGARNPKFSSFYENTDGLHSSLVQIEKSLRTAGQLEGNNNMFLSRVSGGLVDDDHRPFLDENVPVLHLVATPFPDVWHTPRDNAANLHWPSIRNFNRVFRNFVYQYLKRHTSPVNLRFY 338
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191     ||206       216       226       236       246       256       266       276       286       296       306       316       326       336  
                                                                                                                                                                                               197|                                                                                                                                       
                                                                                                                                                                                                203
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4F9U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F9U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F9U)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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        Q9VRQ9_DROME | Q9VRQ9: 4f9v 4fwu

(-) Related Entries Specified in the PDB File

3si2 4f9v 4fai 4fbe